Then and Now
by Regal-Song
Summary: AU. Elizabeth and John went to the same Highschool, though neither ever knew what the other saw in them.
1. Chapter 1

Hey guys, new fic yup! And here is the lovely Disclaimer: I don't own these characters, I don't own Stargate Atlantis, but unfortunately I do own Danny Michaels, if anyone wants to take the little bugger off my hands, you are free to do so!

Chapter 1: High school.

She never saw him, not once. He would watch her as she walked across the quad, her long wavy chocolate hair draping over her shoulders, her eyes sparkling in laughter at something a friend had said.

He studied how she clutched her books to her chest, always was it a large pile.

He watched her in English, as she answered all questions with a raise of her delicate hand, she knew so much about Shakespeare, and he loved how in Ancient History, she always won the weekly knowledge challenges they had.

It was only in math class that he really focused on his work and not her, it was hard, but he was good at math, and his father would never let him fail it.

His cheeks turned crimson once, when she had asked him for help with a complex problem, the jocks had laughed and teased him for being so uncomfortable around her, but he had smiled back at her when she told him to just ignore them.

That had been the first time she had ever spoken to him, when he had seen first hand, her kindness and compassion. After that day he always tried to catch her eye, hoping that maybe she had felt the same thing he had, that spark that shot through his entire being when she was standing mere inches from him.

But she never really spoke to him after that, she would give him a soft smile if ever he said hello, but that was all, mostly he believed it was because of HIM.

Her boyfriend Danny Michaels the captain of the football team, the most handsome guy in school, the most talented football player with the highest grades on the team.

And she was with him, he always had his arm over her shoulders as if he couldn't walk on his own two feet, always trying to kiss her in public, and he had seen all too many times that she had shoved him away with an angry glare. But she never seemed to stay angry for long, giving him a chaste kiss and walking away.

He watched her a lot, and she never really knew. She was the most popular girl in school, every girl wanted to be her, or be her friend, and every guy wanted to date her, or at the very least be awarded that magical smile, so why would she notice a math geek with a crush, whose dark eyes were so often hidden by the hood of his jacket, because his black hair never once liked to cooperate.

She wasn't one of those mindless cheerleaders, and she wouldn't be caught dead worshipping the ground that the school football team walked on.

She loved to learn, she loved to read, and he knew her secret place up on the hill behind the old hall, where she could sit and read one of her novels and no one would disturb her.

She was the smartest and most gorgeous girl he had ever met, and he was in love with her.

He was in love with Elizabeth Weir.

He had never said it out loud and certainly could never tell her, because she only had eyes for Danny, strangely though he thought, because Danny was everything that she wasn't.

He didn't treat her right, and he didn't respect her, she was his trophy nothing more, and it angered him that anyone would treat her as such and inanimate object and it surprised him that she would let him by with it.

He wanted to do something about it, to step out of the shadows and tell her exactly what he thought, that she was better than that, better than anything Danny could give her. But he couldn't tell her that, he was shy, and he knew that Danny was friends with her father, the brutal District attorney, with the mansion in the hills and everything his princess could ever want.

She had a life of luxury, her and her father rattling around in that massive house, they had dinner parties and champagne, she wore beautiful gowns and received endless gifts from her devoted father, while he battled from day to day with his drunken father and irritable mother, their un-mowed lawn and his tiny bedroom filled with model airplanes, he wore the same jacket everyday because his mother refused to buy him new clothes and she wore a new necklace every week because her father had bought it back from a foreign business trip.

He envied her, and he envied her life, but never in a million years would he wish to swap it with her, because they were of separate worlds, separate lives and they suited them, she was perfect in her world and when she every so often drifted into his. And he was flawed in his world, and never did he drift into hers.

He would never forget her, the chills that went up his spine whenever she would pass him in the hall, shivers all over his body when she spoke and the overwhelming feeling to jump up and down whenever she directed her speech to him.

He would never forget her face and he would never forget the day that she was lost to him.

He had been watching her, like he did so often. He watched as she walked behind the grandstand, she looked behind her, making sure no one was following her, she didn't see him, and she walked around the poles until she found what she was looking for.

"Hey" she said with a smile, as the figure before her turned slowly around.

"Hey" he answered as he wrapped his arms around her waist and kissed her deeply. She looked up into his blue eyes as he smiled down at her.

"I've been waiting for you" he said with his lust filled voice deep in his throat. He ran his hands over her body, under her shirt and over the curve of her hips.

"Danny what are you doing?" she asked as he began to kiss the crook of her neck, forcing her head to the side.

"I want you" he muttered pulling at her red scarf and pushing her white corduroy jacket off her shoulders down to her elbows.

"Danny stop" she said trying to squirm out of his grasp. He didn't stop, he held her tighter and she no longer felt safe.

"Danny you're hurting me" she whimpered. And his anger flared he wanted to put a stop to this, but he couldn't move.

Danny shoved her up against the wall and he could see the tears start to form in her beautiful green eyes as Danny's hands pushed underneath her blouse.

She tried to push him away, she tried to fight him, but she wasn't strong enough to push him off her as he captured her lips again.

She almost gagged into his kiss, but he didn't care he kept going.

"You're mine Lizzy, no one else's, you've made me wait long enough" Danny said hoarsely.

He didn't know how she did it, one moment she was slowly breaking, slowly heading towards oblivion of despair, and all of a sudden, Danny was on the ground.

With one swift movement, with one moment of heightened confidence she had thrust her knee into his groin and he had hunched over in pain.

"You will never have me!" she yelled in tears and ran from the stands.

She had run straight past him, holding her jacket tightly around her, wiping at her tears fiercely. He would have sworn he had caught her eye for a moment, but she didn't stop, didn't stop running as Danny called after her.

"You frigid bitch, you weren't even worth it!"

And that was the end of it, he never saw her again.

Her father had transferred her to the private school that she had always refused to attend, rumours passed around the school about her, about where she had gone and why, he ignored them, because he knew the truth.

The very next week Danny had a stupid blonde Barbie on his arm, and it angered him to know that she had meant so little to him, that he had failed to see what he had with her.

Please R&R Guys keeps my paranoia in check!


	2. Chapter 2

Chapter 2: Second Chances

John walked around the cold room, looking at all the scientists studying different pieces of what General O'Neill had called "alien technology" he could hear a man with a Scottish accent explaining the particulars of what he had done mere minutes earlier and he followed the voice.

"_The second I shut my eyes I could see it, I just felt this power I've never had before, it was dancing across the sky…" _he heard the man explain with a chuckle "_it was magical, really it was…"_

"_I don't know where it come from, I just tried to concentrate, and the drone shut itself down" _John finally saw him as he rounded the corner to see the man in the blue jacket standing by a large chair.

"So you were the one?" John asked, and the man turned to him with wide eyes.

"Me?" he asked

"You were the one that fired that thing at me" he said stepping up onto the platform, the man looked at him somewhat in fear of his tone.

He couldn't stress to john enough how sorry he was, and upon seeing this john forgave him in an instant wondering what was going on down here, it was all so very confusing. The man started to explain to him about the ancients, and about a random gene found in some humans that enabled them to operate ancient technology. John slowly wondered in a circle around the chair as the man explained, and he slowly lowered himself into it.

"Major please don't" he said moving quickly towards him.

"Oh come on, what are the odds of me having the same gene as these guys?" he sad brushing off his worry and leaning back in the chair.

Within and instant the entire platform lit up and the chair reclined, and john froze, gripping tightly at the handles.

"Quite slim actually" the man said with his mouth hanging open.

"DR. WEIR!" he called. "Don't move" he ordered him before he ran away.

John was left for a moment with his own thoughts and fears of what was happening, wondering what he had gotten himself into this time, but what pushed to the forefront of that was the name the man had called as he ran off. Dr Weir. He wondered, could it be her, could it be the girl he had loved so many years ago, the face full of tears he had never been able to forget.

Within the span of a minute he came running back, followed by many others, and it was then that he saw her.

Just as beautiful as he remembered, her dark hair still as rich as it had been though much shorter and straighter than all those years before, she was dressed in a deep red jacket and looked at him for a moment, as all the other men stepped ahead of her.

"Who is this?" she asked, and his heart had momentarily crushed, she didn't remember him.

"I told you not to touch anything" General O'Neill said and john stuttered, tearing his eyes away from her.

"I-I just sat down"

The whole moment was a bit overwhelming, he imagined where they were in the solar system, and it appeared before there eyes in a beautiful hologram suspended in the air. He could see out of the corner of his eye that she was smiling, not her full blown one, but it was gorgeous all the same.

She asked him to go with her, on this expedition to another galaxy, never in a million years would he think she would be asking him this, or anything for that matter, she looked at him with those big deep green eyes, and he found it difficult to say no, though every time he looked at her he was reminded of that day behind the grandstand, when he was in the position to help her and he couldn't do it.

He felt ashamed that he couldn't help the person he had loved the most in the world, ashamed of what she would think of him if she ever found out. But here she was, asking him, him of all people to follow her to another world, on an amazing adventure, and her eyes sparkled with excitement.

General O'Neill, practically ordered him to go, and he knew that he was right, it was an amazing opportunity, but he was afraid.

He wasn't afraid of the distant galaxy, of the endless black and foreign stars, he wasn't afraid of all the possible dangers that he would no doubt face. No. he was afraid of one thing and one thing only. Elizabeth.

He was afraid of it all happening again, of being there, of seeing her in danger all over again, and being powerless to stop it.

He couldn't face it; he couldn't face her, after all these years and she didn't even recognise him, but he couldn't bare it.

But here he is, at the base of the stairs with Carson behind him, and Elizabeth ahead of them addressing the entire expedition team, with her head high and her voice strong.

He was really going, really taking that step if only to be that little bit closer to her after so many years of wondering what had happened to her.

They arrived on Atlantis and he followed her everywhere, he watched over her, there were plenty of other military officers to explore, his job was to watch over her.

Not everything was smooth sailing, and he felt stupid to ever think it would be, because as soon as they stepped through the gate, the power levels started to drop, they called back the security teams and they tried all sorts of ways to channel the power but nothing worked, the city was dying, and they were going to drown.

Elizabeth ordered them in search of safe harbour, or better yet, another power source, though john had no intention of leaving, not if she was intending to stay.

"Major I'd like you to go with them" Damn, he thought, as she gave him that order, if only she hadn't asked, if she hadn't asked, he wouldn't have had to leave her there. But he gathered himself, and he prepared himself to take that step. Waving to her as he left, he stepped through the gate again.

He met the Athosian people, Teyla and Halling, and his son Jinto, Teyla explained about the beings called wraiths, a powerful and formidable enemy, and he felt his skin crawl at their mere description.

Teyla walked him to the old ruins, though all he thought about on their journey was Elizabeth, was she alright, was he taking too long.

As they headed back to the village John heard lieutenant ford over the radio, that there were multiple bogies headed in their direction. He and Teyla immediately broke into a run, she was faster, leaping and bounding over rocks and fallen logs, as he scrambled his way desperately trying to keep up with her.

They were all around him, he could feel them, he could see their silhouettes moving in the mist, strange and terrifying figures playing with his eyes and he stopped, he raised his weapon, but he couldn't figure out where to fire.

His eyes widened as Teyla returned to him, spreading the shadows as she went, stating "the wraith make you see things that are not there"

And they were running again, he told Colonel Sumner to fire on the ships, and to his knowledge he did, regardless of the mans dislike of him.

Many of Teyla's people were killed, and many more taken to be fed upon, it was a horrifying thought. Colonel Sumner, Bates, Teyla and Halling were all taken. John found Jinto on the beach by some Wraith wreckage as a wraith arm crawled along the ground on its own.

For a moment he didn't know what to do, the place was in ruins, the people were shattered and John was in way over his head. Then he looked into the eyes of that frightened young boy, and he did what he knew was right.

They gathered the remaining people at the gate, and he took them back to Atlantis, he saw Elizabeth as she ran down the stairs to him, the city was shaking and rumbling, and she looked absolutely terrified.

"Major Sheppard, who are all these people?" she asked angrily

"Survivors from the settlement, we were attacked; Sumner and some of our men were taken…what's going on?"

She grabbed him by the arm and pulled him towards her.

"We are in no position to help anyone right now" she said in a low voice.

"What the hell's going on here?" he asked looking up at the ceiling, and the walls shaking.

"We are about the abandon the city" she stated, and he looked down into her eyes.

"Going back there is a really bad idea"

"Major Sheppard the shield is about the fail and the ocean is about to come _crashing _in on us, do you have a better place for us to go?" she asked and he could see the genuine fear in her eyes.

Quickly he turned around.

"Jinto, do you know of any other addresses we can gate to?" he asked.

"Yes, many" he answered.

John grabbed Jinto by the arm and they ran for the stairs, Elizabeth was sceptical, but he pushed on. John turned around suddenly, dropping to his knees as the entire city shook with an amazing force, he saw behind him as Elizabeth fell backwards onto the floor, her legs flying in the air before she hit the ground but he found it necessary to stay and hold Jinto to the stairs. He was relieved as he saw Lieutenant Ford hold Elizabeth on her feet, as the great city began to rise.

"We're moving!" he shouted as they could see the water rushing over the windows. Boxes fell and people staggered to stay on their feet.

"_I'm Dialling and address"_ they heard Grodin in the control room.

"NO WAIT!" Elizabeth screamed, and he did.

The massive city exploded out of the surface of the ocean, great monolithic towers rose as beams of sunlight shot through the patchwork windows showering the massive room in all sorts of marvellous colours.

Once the city finally came to a stop, it was on the surface of the ocean, water trickled down the windows as people looked out over the endless expanse of sea.

John watched Elizabeth as she slowly made her way up the stairs, starring out the window in awe as they all were.

"I was hoping for another day…"she breathed out "looks like we just got a whole lot more than that, lets not waste it" she said and John smiled.

He wasn't going to waste it. This was his second chance, new city, new galaxy, new terrors, and the same Elizabeth. It was his chance to make it right.

She may not remember him; she may not remember the young boy who followed her around at school, who was too afraid to speak to her, too afraid to help her when she needed it the most. But he was different now, he was older, stronger, and more confident, some would even say cocky, and he wanted nothing more than to help her see him this time.

Please R&R


	3. Chapter 3

Chapter 3: The choices we make.

Elizabeth listened intently as Rodney explained that while they did have limited power for now, the city had no way to power the shield. That slightly unnerved her, and as John stated that they were "Target practice" and Rodney answered.

"I'm acutely aware of that major, but thankyou for reinforcing it" she had to close her eyes and shake her head. She could sense the bickering a mile away.

Because they were so alike, John and Rodney, both so intelligent and passionate, and neither one outwardly wanted to be like the other.

She could see it in Rodney from the moment she met him, he was so much like what John used to be, the dark genius, though of course Rodney was rude and arrogant,_ that_ john had never been.

As soon as she saw John there sitting in that chair, she knew that she recognised those eyes, at the time she couldn't put his face to a name, or a specific memory, but it was there, gnawing at her, his eyes burning into her. She had asked who he was, and she would have sworn that for a moment, a wash of disappointment clouded his eyes.

She had wondered at the time if perhaps he had known it too, that there was something there, some faint recognition.

But now, after this day, after coming through the Stargate and seeing this city, so preserved, so pristine and fearing that they might have to run away from it. Seeing John go off on that mission and bringing back the group of Athosians, bruised and beaten, she knew it was him, she could see it in his eyes, in his wild hair, she could see the boy that high society told her she could never know.

He had always intrigued her, the wonder of the unknown. He was so dirty so mysterious, shadowed by that black hooded jacket that always hid his beautiful dark eyes. And here he was, all these years had passed since the day she saw him last, and he was so different, yet, she could still see the boy in him, the geek in him.

"When can you tell me where the wraith took Colonel Sumner and the others?" she heard him ask Rodney, and she knew that he was now a fighter.

"Even with the six symbols lt. Ford provided, there are still hundreds of permutations that…"

"720" he cut him off and Rodney silenced for a moment. But he was still a geek, and she had to hide a slight smile that grew on her lips.

Elizabeth led him across the control room, intent to find a place where she could speak to him in private, but a door suddenly opened and they looked upon the large balcony.

Elizabeth glanced at John before stepping out, they walked carefully across it as the floor as still coated in puddles.

"Let me guess…you aren't gonna let me rescue my people?" he asked as they both lent heavily on the railing.

"Major, you don't even know if they're alive" she said as she slowly turned to him.

"You don't leave people in the hands of the enemy…and the fact that we are having this conversation In private tells me that you know damn well that it's wrong and it will totally undermine your leadership" she couldn't believe it, is this really what he thought of her?

"So as ranking military officer…" she couldn't let him continue. So she cut him off.

"Ok, just shut up! And listen to me for a moment alright"

"Come on what do we know about the wraith, one of the few things we do know is that they are the enemy that defeated the Ancients"

She explained to him the ramifications of the first time that they used the Stargate on Earth, the troubles that they caused for earth were immeasurable, and that was her point. She didn't want those people to die; she didn't want anyone to die, she just needed more information.

"I will not authorise a rescue mission unless I am sure there is at least a remote chance of success, I'm not sending more good people including you, to their deaths" she couldn't help the slip, she needed to get her point across and by addressing him directly, stressing how much she needed him to stay alive, maybe he would see what she had always felt, and what she felt now that she was responsible for his life and the lives of all of those people he so desperately wanted to save.

"Ok" was all he said before he left her alone on that balcony.

They did go through with the mission, John found a bay of ships that he easily figured out how to operate, and the decision was made.

She watched as the lowered into the room, and she watched as it disappeared through the event horizon.

"Be safe" she whispered as the gate shut down, and he was once again gone.

She worried about them the entire time they were gone, but they returned, safe and in one piece, but Colonel Sumner didn't make it.

John told her what had happened, how he had taken the colonel's life, and he could never forgive himself. She knew that it must have been difficult for him, but hs didn't even try to tell him that she understood, because there was no way that she could.

All she could do now was tell him the one thing that she had been wanting to tell him since she realised exactly who he was.

She lent her elbows on the railing and he did the same.

"You know I knew you were there that day" she stated, fiddling with the handle of her mug.

"What?" he asked looking sideways at her, but she didn't turn her head.

"That day behind the grandstand…I knew that you were there" john nearly choked on his wine.

"What! Then why...I thought that you…I mean, I didn't know you remembered…" he stuttered and didn't make much sense, Elizabeth slowly turned her head to the side with a smirk and he calmed a little.

"Elizabeth, I…" she waved him off.

"John its ok" he stood straighter, and looked at her closely.

"No it isn't ok, he hurt you and I couldn't do anything, I froze" he explained.

"John, Danny was…" he cut her off.

"Danny was a jerk!" she startled a little and stood to face him. "He never cared about you, I could see it everyday, he was a pig and he used you" Elizabeth dropped her chin to her chest, and he could see the sadness in her eyes. "He didn't deserve you" he breathed out, and she slowly looked up at him again.

"Elizabeth, I'm sorry I couldn't help you then, I was afraid of you, I was afraid of the life that you had, you were way out of my league, and seeing you now…I know that you still are" Elizabeth blushed only slightly "but I hope that maybe, if you let me, I can make it up to you."

"John you don't have to…" he cut her off again.

"yes!...I do, because all I have seen for the past 20 years is your face, when ever I fall asleep I can see the tears in your eyes as you ran past me, I've never been able to shake it"

Elizabeth just studied him for a moment, looking deep into his eyes, as he looked deep into hers waiting for her to say something.

"Then I want to make it up to you as well" she said softly, and john looked confused.

"For what, you never did anything wrong…" she stopped him with sadness in her eyes.

"Yes I did, I loved you" he stood unevenly for a moment. "I loved you all through high school, but I was afraid of what it would mean, my father would never have approved, and that's why I was with Danny…I never loved him, after I left I couldn't bare the thought of what I had done to you" john was caught off guard, he never thought she felt that way, never in his wildest dreams did he think that she could ever care for him as much as he did her.

"And now?" he found himself asking, though his brain hadn't registered what he was saying. She looked away down at the ocean, deep in thought.

"I don't know, you are so different, I'm so different…" she breathed out deeply

"You're still beautiful" he said beneath a whisper and she looked up into his eyes, he could see pain in them, like he had said the wrong thing, and she stepped back, twisting her fingers in her hand with her face scrunched.

"But Simon…"she trailed off and John reached a realisation, she was with someone.

"You…?"

"Yes" she cut him off

"Elizabeth I'm sorry…"

"don't be, I'm not…I care about Simon, I really do…but I have loved you for so many years…I just don't know what to do" she said.

John stepped up to her, moving further and further into her personal space, but he didn't care, and she just looked up into his eyes, as the tears began to form in hers. Gently he brushed a lock of hair from her face, and tucked it behind her ear, leaving his hand cupped against her cheek.

"don't worry about it Elizabeth, you don't have to decide anything right now, just know that I am here, and I'm not going to make the same mistake I did 20 years ago. And whatever you decide, I'll always be here, waiting for you."

"John…"she trailed off as his thumb caressed her cheek.

"Simon or me, it doesn't matter, as long as you make the choice that makes you happy, I'm here for you, and I'll always be your friend Elizabeth, as long as you'll have me"

Elizabeth studied him closely trailing her eyes across every line on his face, every whisker on his only slightly stubbled chin, she studied the young sparkle in his eye that he had all those years ago, and she realised that he wasn't so different, he wasn't so foreign that she couldn't fall in love with him all over again.

And then it hit her, she had never stopped loving him, she cared for Simon and she hated to hurt him, but she was in another galaxy, and she had told him to move on with his life, she couldn't pass up this chance to start over with john, for her mistakes to be forgiven and star anew.

And she couldn't expect Simon to wait forever anyway.

"John, I…I think I still feel…" he moved his hand from her cheek to the nape of her neck and he could feel the heat there.

"I think I still…"she was breathing heavily and so was he as he slowly leaned closer to her, her eyes shifted from his eyes to his lips as he got closer and suddenly her words eluded her.

"Love you" he finished for her, as his lips touched hers ever so softly.

"Mhmm" she answered into the kiss that deepened and sent electrifying shivers through her body.

"me too" he whispered as their lips parted long enough for him to say just that, and then drew back to each other for another deeper kiss as his arms curled around her waist.

"But what about…"

"shhh" he said stroking her cheek "we'll work it out" and she smiled as she lent her head down to rest it on his chest as he wrapped his arms around her tighter, holding her as the breeze of Atlantis ruffled there hair and brought glimpse of new adventures, possibilities of new wonders to be discovered, because the best part of their lives…had only just begun.

The End.


End file.
